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It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.
Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy
http://www.nitrc.org/projects/asdb/
Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools.
Proper citation: Altered States Database (RRID:SCR_016350) Copy
https://www.genome.jp/kegg/pathway.html
Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development.
Proper citation: KEGG PATHWAY Database (RRID:SCR_018145) Copy
Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.
Proper citation: CellPhoneDB (RRID:SCR_017054) Copy
Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.
Proper citation: Database of Open Chromatin Regions (RRID:SCR_016614) Copy
http://omicslab.genetics.ac.cn/dred/index.php
Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.
Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy
Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).
Proper citation: mqtldb (RRID:SCR_018002) Copy
Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.
Proper citation: PostgreSQL (RRID:SCR_021067) Copy
Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines.
Proper citation: Scopus (RRID:SCR_022559) Copy
https://github.com/clinwiki-org/clinwiki
Clinical trials database.
Proper citation: ClinWiki (RRID:SCR_021297) Copy
Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.
Proper citation: trinetx (RRID:SCR_022760) Copy
Ratings or validation data are available for this resource
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.
Proper citation: Trim Galore (RRID:SCR_011847) Copy
Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.
Proper citation: Apache Spark (RRID:SCR_016557) Copy
https://github.com/facebook/prophet
Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.
Proper citation: Prophet (RRID:SCR_017083) Copy
Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.
Proper citation: Data Biosphere (RRID:SCR_016154) Copy
http://reproducibility.stanford.edu/
Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.
Proper citation: Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) Copy
https://github.com/TeamMacLean/atacr
Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.
Proper citation: atacr (RRID:SCR_016286) Copy
https://github.com/kstreet13/slingshot
Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.
Proper citation: Slingshot (RRID:SCR_017012) Copy
Ratings or validation data are available for this resource
https://github.com/BodenmillerGroup/imctools
Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.
Proper citation: imctools (RRID:SCR_017132) Copy
https://github.com/colinvaz/nmf-toolbox
Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.
Proper citation: NMF Toolbox (RRID:SCR_017069) Copy
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